Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1029 ID=scaffold_1029-JGI_221_v2.0

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 852

Length: 1420
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40


Found at i:610 original size:9 final size:9

Alignment explanation


    Indices: 531--627  Score: 51
    Period size: 9  Copynumber: 10.6  Consensus size: 9

        521 TCTTCTTCTT

                     
        531 TTTTTA-AA
          1 TTTTTATAA

                  *   
        539 TTTTTTGTAA
          1 -TTTTTATAA

                       
        549 TTTGTTAGTAA
          1 TTT-TTA-TAA

                       
        560 CTTTTATATAA
          1 -TTTT-TATAA

                     
        571 -TTTTAT--
          1 TTTTTATAA

                 *    
        577 TTTCTAATAA
          1 TTT-TTATAA

                      
        587 TTTTATATAA
          1 TTTT-TATAA

                   * 
        597 TTTTTATTA
          1 TTTTTATAA

                  *  
        606 TTTTTAAAA
          1 TTTTTATAA

                *    
        615 TTTTAAT-A
          1 TTTTTATAA

                 
        623 TTTTT
          1 TTTTT

        628 TCTATAAGTT


Statistics
Matches: 68,  Mismatches: 10, Indels: 21
        0.69            0.10        0.21

Matches are distributed among these distances:
   7    2  0.03
   8   11  0.16
   9   28  0.41
  10   15  0.22
  11    7  0.10
  12    5  0.07

ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64


Consensus pattern (9 bp):   
TTTTTATAA
Done.